Implementation of dynamic coupling in hybrid Molecular Dynamics–Lattice Boltzmann approach: Modeling aggregation of amphiphiles

Xiang Yu, Meenakshi Dutt

Research output: Contribution to journalArticlepeer-review

Abstract

Amphiphile-based aggregates are extensively used in numerous applications for encapsulation, storage, transport and delivery of toxic, active molecules due to the structural properties of the aggregates. The properties of the aggregates in turn are dictated by the molecular architecture of the amphiphiles. A complete understanding of the multiscale architecture–structure–function relationship for amphiphile-based aggregates requires the simultaneous resolution of the self-assembly of amphiphilic molecules along with an understanding of the role of various long range physical interactions including hydrodynamics. A multiscale computational approach such as the hybrid Molecular Dynamics–Lattice Boltzmann technique is able to fulfill most of those requirements. However, existing implementations only account for static coupling between the Molecular Dynamics technique and the Lattice Boltzmann method, and hence are unable to resolve the changes in the solvent-amphiphile interface during processes such as self-assembly and interfacial adsorption. In this study, a new implementation incorporating a dynamic coupling scheme between the Molecular Dynamics technique and the Lattice Boltzmann method is introduced so as to resolve dynamical changes in interfaces. The application of the new implementation to the self-assembly of phospholipids yields results which are in good agreement with computation, experiments and theory. In particular, we found the scaling exponent α of the cluster number (N(t) = C tα) to be ∼1. Program summary: Program Title: fix_lb_fluid_dynamic_coupling.cpp, fix_lb_fluid_dynamic_coupling.h Program Files doi: http://dx.doi.org/10.17632/wr4mgv35j5.1 Licensing provisions: GNU General Public License 3 Programming language: C++ Journal Reference of previous version: Mackay, F. E., Ollila, S. T., & Denniston, C. (2013). Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid. Computer Physics Communications, 184(8), 2021-2031. Does the new version supersede the previous version? No. Reasons for new version: Enable dynamic coupling between Molecular Dynamics and Lattice Boltzmann. Summary of revisions: Determination of whether the number of neighbors for each Molecular Dynamics bead is above a predetermined threshold set by the user. If the number of neighbors is above the threshold, the Molecular Dynamics bead is decoupled from the Lattice Boltzmann grid. Nature of problem: Determination of the criteria and method for decoupling Molecular Dynamics beads from the Lattice Boltzmann grid. Solution method: The number of neighbors for each Molecular Dynamics bead which lie within the interaction potential cutoff distance is determined. If the number of neighbors is above a critical threshold, the reference Molecular Dynamics bead is decoupled from the Lattice Boltzmann grid.

Original languageEnglish (US)
Article number107287
JournalComputer Physics Communications
Volume257
DOIs
StatePublished - Dec 2020

All Science Journal Classification (ASJC) codes

  • Hardware and Architecture
  • Physics and Astronomy(all)

Keywords

  • Amphiphiles
  • Dynamic coupling
  • LAMMPS
  • Martini-based implicit solvent coarse-grained force field
  • Molecular Dynamics–Lattice Boltzmann
  • Phospholipids

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